Drug similarity and structure-based screening of medicinal compounds to target macrodomain-I from SARS-CoV-2 to rescue the host immune system: a molecular dynamics study
文献类型：期刊论文
| 作者 | Babar, Zainib8; Zahra, Mubeen8; Khan, Mazhar7; Anwar, Munazza6; Noor, Kashif5; Suleman, Muhammad4; Ali, Shahid4; Ali, Syed Shujait4; Shah, Abdullah3; Hashmi, Huma Farooque2 |
| 刊名 | JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
 |
| 关键词 | FREE-ENERGY CALCULATIONS ADP-RIBOSE REPLICATION BINDING CORONAVIRUSES SOFTWARE DOCKING AMBER |
| ISSN号 | 0739-1102 |
| DOI | 10.1080/07391102.2020.1815583 |
| 文献子类 | Article; Early Access |
| 英文摘要 | The outbreak of the recent coronavirus (SARS-CoV-2), which causes a severe pneumonia infection, first identified in Wuhan, China, imposes significant risks to public health. Around the world, researchers are continuously trying to identify small molecule inhibitors or vaccine candidates by targeting different drug targets. The SARs-CoV-2 macrodomain-I, which helps in viral replication and hijacking the host immune system, is also a potential drug target. Hence, this study targeted viral macrodomain-I by using drug similarity, virtual screening, docking and re-docking approaches. A total of 64,043 compounds were screened, and potential hits were identified based on the docking score and interactions with the key residues. The top six hits were subjected to molecular dynamics simulation and Free energy calculations and repeated three times each. The per-residue energy decomposition analysis reported that these compounds significantly interact with Asp22, Ala38, Asn40, Val44, Phe144, Gly46, Gly47, Leu127, Ser128, Gly130, Ile131, Phe132 and Ala155 which are the critical active site residues. Here, we also used ADPr as a positive control to compare our results. Our results suggest that our identified hits by using such a complicated computational pipeline could inhibit the SARs-CoV-2 by targeting the macrodomain-1. We strongly recommend the experimental testing of these compounds, which could rescue the host immune system and could help to contain the disease caused by SARs-CoV-2. Communicated by Ramaswamy H. Sarma |
| 学科主题 | Biochemistry & Molecular Biology ; Biophysics |
| WOS关键词 | Macrodomain-I ; immune system ; SARs-CoV-2 ; drug similarity ; free energy |
| 语种 | 英语 |
| WOS记录号 | WOS:000567558000001 |
| 版本 | 出版稿 |
| 源URL | [http://202.127.25.143/handle/331003/3587]  |
| 专题 | 生化所2019-2020年发文 |
| 作者单位 | 1.Riphah Int Univ, Fac Rehabil & Allied Hlth Sci, Islamabad, Pakistan, 2.Shandong Univ, Sch Life Sci, Jinan, Shandong, Peoples R China; 3.Shaheed Benazir Bhutto Univ, Dept Biotechnol, Sheringal, Dir, Pakistan; 4.Univ Swat, Ctr Biotechnol & Microbiol, Swat, Khyber Pakhtunk, Pakistan; 5.Univ Agr Faisalabad, Dept Plant Breeding & Genet, Punjab, Pakistan; 6.Quaid I Azam Univ, Fac Biol Sci, Dept Biochem, Islamabad, Pakistan; 7.Univ Sci & Technol China USTC, CAS Ctr Excellence Mol Cell Sci, Collaborat Innovat Ctr Genet & Dev,Hefei Natl Lab, Sch Life Sci,CAS Key Lab Innate Immun & Chron Dis, Hefei, Anhui, Peoples R China; 8.Univ Agr Faisalabad, Dept Bot, Faisalabad, Punjab, Pakistan; |
| 推荐引用方式 GB/T 7714 | Babar, Zainib,Zahra, Mubeen,Khan, Mazhar,et al. Drug similarity and structure-based screening of medicinal compounds to target macrodomain-I from SARS-CoV-2 to rescue the host immune system: a molecular dynamics study[J]. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS. |
| APA | Babar, Zainib.,Zahra, Mubeen.,Khan, Mazhar.,Anwar, Munazza.,Noor, Kashif.,...&,. |
| MLA | Babar, Zainib,et al."Drug similarity and structure-based screening of medicinal compounds to target macrodomain-I from SARS-CoV-2 to rescue the host immune system: a molecular dynamics study".JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS |
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